scholarly journals Computational modelling of chromosome re-replication in mutant strains of fission yeast

2020 ◽  
Author(s):  
Béla Novák ◽  
John J Tyson
Keyword(s):  
Dna Replication ◽  
Fission Yeast ◽  
Computational Modelling ◽  
Mitotic Cell ◽  
Cyclin Dependent Kinase ◽  
Slow Increase ◽  
Cell Cycles ◽  
Mitotic Cyclin ◽  
The Mathematical Model ◽  
Insight Into

AbstractTypically cells replicate their genome only once per division cycle, but under some circumstances, both natural and unnatural, cells synthesize an overabundance of DNA, either in a disorganized fashion (‘over-replication’) or by a systematic doubling of chromosome number (‘endoreplication’). These variations on the theme of DNA replication and division have been studied in strains of fission yeast, Schizosaccharomyces pombe, carrying mutations that interfere with the function of mitotic cyclin-dependent kinase (Cdk1:Cdc13) without impeding the roles of DNA-replication licensing factor (Cdc18) and S-phase cyclin-dependent kinase (Cdk1:Cig2). Some of these mutations support endoreplication, and some over-replication. In this paper, we propose a dynamical model of the interactions among the proteins governing DNA replication and cell division in fission yeast. By computational simulations of the mathematical model, we account for the observed phenotypes of these re-replicating mutants, and by theoretical analysis of the dynamical system, we provide insight into the molecular distinctions between over-replicating and endoreplicating cells. In case of induced over-production of regulatory proteins, our model predicts that cells first switch from normal mitotic cell cycles to growth-controlled endoreplication, and ultimately to disorganized over-replication, parallel to the slow increase of protein to very high levels.

scholarly journals DNA Replication Origins Fire Stochastically in Fission Yeast

2006 ◽  
Vol 17 (1) ◽  
pp. 308-316 ◽  
Author(s):  
Prasanta K. Patel ◽  
Benoit Arcangioli ◽  
Stephen P. Baker ◽  
Aaron Bensimon ◽  
Nicholas Rhind
Keyword(s):  
Dna Replication ◽  
Fission Yeast ◽  
Replication Initiation ◽  
Epigenetic Mechanism ◽  
Replication Origins ◽  
Origin Firing ◽  
Cell Cycles ◽  
Initiation Of Replication ◽  
Dna Combing ◽  
Dna Replication Origins

DNA replication initiates at discrete origins along eukaryotic chromosomes. However, in most organisms, origin firing is not efficient; a specific origin will fire in some but not all cell cycles. This observation raises the question of how individual origins are selected to fire and whether origin firing is globally coordinated to ensure an even distribution of replication initiation across the genome. We have addressed these questions by determining the location of firing origins on individual fission yeast DNA molecules using DNA combing. We show that the firing of replication origins is stochastic, leading to a random distribution of replication initiation. Furthermore, origin firing is independent between cell cycles; there is no epigenetic mechanism causing an origin that fires in one cell cycle to preferentially fire in the next. Thus, the fission yeast strategy for the initiation of replication is different from models of eukaryotic replication that propose coordinated origin firing.

scholarly journals Establishment of expression-state boundaries by Rif1 and Taz1 in fission yeast

2017 ◽  
Vol 114 (5) ◽  
pp. 1093-1098 ◽  
Author(s):  
Tea Toteva ◽  
Bethany Mason ◽  
Yutaka Kanoh ◽  
Peter Brøgger ◽  
Daniel Green ◽  
...  
Keyword(s):  
Dna Replication ◽  
Fission Yeast ◽  
Replication Timing ◽  
Genetic Screens ◽  
Origin Firing ◽  
Regulate Gene Expression ◽  
Boundary Formation ◽  
Amino Terminal ◽  
Amino Terminal Domain ◽  
Insight Into

The Shelterin component Rif1 has emerged as a global regulator of the replication-timing program in all eukaryotes examined to date, possibly by modulating the 3D-organization of the genome. In fission yeast a second Shelterin component, Taz1, might share similar functions. Here, we identified unexpected properties for Rif1 and Taz1 by conducting high-throughput genetic screens designed to identifycis-andtrans-acting factors capable of creating heterochromatin–euchromatin boundaries in fission yeast. The preponderance ofcis-acting elements identified in the screens originated from genomic loci bound by Taz1 and associated with origins of replication whose firing is repressed by Taz1 and Rif1. Boundary formation and gene silencing by these elements required Taz1 and Rif1 and coincided with altered replication timing in the region. Thus, small chromosomal elements sensitive to Taz1 and Rif1 (STAR) could simultaneously regulate gene expression and DNA replication over a large domain, at the edge of which they established a heterochromatin–euchromatin boundary. Taz1, Rif1, and Rif1-associated protein phosphatases Sds21 and Dis2 were each sufficient to establish a boundary when tethered to DNA. Moreover, efficient boundary formation required the amino-terminal domain of the Mcm4 replicative helicase onto which the antagonistic activities of the replication-promoting Dbf4-dependent kinase and Rif1-recruited phosphatases are believed to converge to control replication origin firing. Altogether these observations provide an insight into a coordinated control of DNA replication and organization of the genome into expression domains.

Inhibition of cysteine protease activity disturbs DNA replication and prevents mitosis in the early mitotic cell cycles of sea urchin embryos

2005 ◽  
Vol 204 (2) ◽  
pp. 693-703 ◽  
Author(s):  
Carolina Concha ◽  
Antonia Monardes ◽  
Yasmine Even ◽  
Violeta Morin ◽  
Marcia Puchi ◽  
...  
Keyword(s):  
Dna Replication ◽  
Sea Urchin ◽  
Cysteine Protease ◽  
Protease Activity ◽  
Mitotic Cell ◽  
Cell Cycles ◽  
Sea Urchin Embryos ◽  
Cysteine Protease Activity

Differential function and expression of Saccharomyces cerevisiae B-type cyclins in mitosis and meiosis

1993 ◽  
Vol 13 (4) ◽  
pp. 2113-2125
Author(s):  
N Grandin ◽  
S I Reed
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Cell Cycle ◽  
Kinase Activity ◽  
Mitotic Cell ◽  
S Phase ◽  
Mitotic Cell Cycle ◽  
Meiotic Cell ◽  
Cell Cycles ◽  
M Phase ◽  
Mitotic Cyclin

We have studied the patterns of expression of four B-type cyclins (Clbs), Clb1, Clb2, Clb3, and Clb4, and their ability to activate p34cdc28 during the mitotic and meiotic cell cycles of Saccharomyces cerevisiae. During the mitotic cell cycle, Clb3 and Clb4 were expressed and induced a kinase activity in association with p34cdc28 from early S phase up to mitosis. On the other hand, Clb1 and Clb2 were expressed and activated p34cdc28 later in the mitotic cell cycle, starting in late S phase and continuing up to mitosis. The pattern of expression of Clb3 and Clb4 suggests a possible role in the regulation of DNA replication as well as mitosis. Clb1 and Clb2, whose pattern of expression is similar to that of other known Clbs, are likely to have a role predominantly in the regulation of M phase. During the meiotic cell cycle, Clb1, Clb3, and Clb4 were expressed and induced a p34cdc28-associated kinase activity just before the first meiotic division. The fact that Clb3 and Clb4 were not synthesized earlier, in S phase, suggests that these cyclins, which probably have a role in S phase during the mitotic cell cycle, are not implicated in premeiotic S phase. Clb2, the primary mitotic cyclin in S. cerevisiae, was not detectable during meiosis. Sporulation experiments on strains deleted for one, two, or three Clbs indicate, in agreement with the biochemical data, that Clb1 is the primary cyclin for the regulation of meiosis, while Clb2 is not involved at all.

scholarly journals The G1/S Cyclin Cig2p during Meiosis in Fission Yeast

2002 ◽  
Vol 13 (6) ◽  
pp. 2080-2090 ◽  
Author(s):  
Annie Borgne ◽  
Hiroshi Murakami ◽  
José Ayté ◽  
Paul Nurse
Keyword(s):  
Fission Yeast ◽  
S Phase ◽  
Start Site ◽  
Meiotic Cell ◽  
Transcription Start ◽  
Cell Cycles ◽  
Cyclin Dependent Kinases ◽  
Mitotic Cyclin ◽  
Specific Regulation

Cyclin-dependent kinases (CDKs) are important for both mitotic and meiotic cell cycles. In fission yeast, the major CDK, Cdc2p is involved in premeiotic DNA replication and in meiosis II. One of its partners, the mitotic cyclin Cdc13p is known to be required for meiosis, whereas there are no studies on the G1/S cyclin Cig2p. In this article, we have studied the regulation of the Cdc2p/Cdc13p and Cdc2p/Cig2p complexes during synchronous meiosis. We observed that Cdc2p/Cig2p kinase is activated in an unexpected biphasic manner, first at onset of premeiotic S phase and again during meiotic nuclear divisions. The role of Cig2p during meiosis was investigated usingcig2-deleted strains that exhibit delays in onset of both S phase and meiotic divisions as well as an inefficient completion of MII. Furthermore, analysis of cig2 transcripts revealed a meiosis-specific regulation of cig2expression during MI/MII dependent upon the Mei4p transcription factor leading to a different transcription start site at this stage of meiosis.

scholarly journals The Hsk1(Cdc7) Replication Kinase Regulates Origin Efficiency

2008 ◽  
Vol 19 (12) ◽  
pp. 5550-5558 ◽  
Author(s):  
Prasanta K. Patel ◽  
Naveen Kommajosyula ◽  
Adam Rosebrock ◽  
Aaron Bensimon ◽  
Janet Leatherwood ◽  
...  
Keyword(s):  
Dna Replication ◽  
Fission Yeast ◽  
Genomic Instability ◽  
Chromatin Structure ◽  
Replication Timing ◽  
Local Concentration ◽  
Origin Firing ◽  
Cell Cycles ◽  
Firing Rates ◽  
Rate Limiting

Origins of DNA replication are generally inefficient, with most firing in fewer than half of cell cycles. However, neither the mechanism nor the importance of the regulation of origin efficiency is clear. In fission yeast, origin firing is stochastic, leading us to hypothesize that origin inefficiency and stochasticity are the result of a diffusible, rate-limiting activator. We show that the Hsk1-Dfp1 replication kinase (the fission yeast Cdc7-Dbf4 homologue) plays such a role. Increasing or decreasing Hsk1-Dfp1 levels correspondingly increases or decreases origin efficiency. Furthermore, tethering Hsk1-Dfp1 near an origin increases the efficiency of that origin, suggesting that the effective local concentration of Hsk1-Dfp1 regulates origin firing. Using photobleaching, we show that Hsk1-Dfp1 is freely diffusible in the nucleus. These results support a model in which the accessibility of replication origins to Hsk1-Dfp1 regulates origin efficiency and provides a potential mechanistic link between chromatin structure and replication timing. By manipulating Hsk1-Dfp1 levels, we show that increasing or decreasing origin firing rates leads to an increase in genomic instability, demonstrating the biological importance of appropriate origin efficiency.

scholarly journals Cdc28 and Ime2 Possess Redundant Functions in Promoting Entry Into Premeiotic DNA Replication in Saccharomyces cerevisiae

Genetics ◽  
2001 ◽  
Vol 159 (4) ◽  
pp. 1547-1558
Author(s):  
Noga Guttmann-Raviv ◽  
Elisabeth Boger-Nadjar ◽  
Iris Edri ◽  
Yona Kassir
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Dna Replication ◽  
Meiotic Recombination ◽  
Mitotic Cell ◽  
Temperature Sensitive ◽  
Cyclin Dependent Kinase ◽  
Yeast Saccharomyces Cerevisiae ◽  
Redundant Functions ◽  
Meiotic Cycle

Abstract In the budding yeast Saccharomyces cerevisiae initiation and progression through the mitotic cell cycle are determined by the sequential activity of the cyclin-dependent kinase Cdc28. The role of this kinase in entry and progression through the meiotic cycle is unclear, since all cdc28 temperature-sensitive alleles are leaky for meiosis. We used a “heat-inducible Degron system” to construct a diploid strain homozygous for a temperature-degradable cdc28-deg allele. We show that this allele is nonleaky, giving no asci at the nonpermissive temperature. We also show, using this allele, that Cdc28 is not required for premeiotic DNA replication and commitment to meiotic recombination. IME2 encodes a meiosis-specific hCDK2 homolog that is required for the correct timing of premeiotic DNA replication, nuclear divisions, and asci formation. Moreover, in ime2Δ diploids additional rounds of DNA replication and nuclear divisions are observed. We show that the delayed premeiotic DNA replication observed in ime2Δ diploids depends on a functional Cdc28. Ime2Δ cdc28-4 diploids arrest prior to initiation of premeiotic DNA replication and meiotic recombination. Ectopic overexpression of Clb1 at early meiotic times advances premeiotic DNA replication, meiotic recombination, and nuclear division, but the coupling between these events is lost. The role of Ime2 and Cdc28 in initiating the meiotic pathway is discussed.

scholarly journals THE ROLE OF RADIATION (rad) GENES IN MEIOTIC RECOMBINATION IN YEAST

Genetics ◽  
1980 ◽  
Vol 94 (1) ◽  
pp. 51-68
Author(s):  
J C Game ◽  
T J Zamb ◽  
R J Braun ◽  
M Resnick ◽  
R M Roth
Keyword(s):  
Dna Replication ◽  
Dna Synthesis ◽  
Gene Conversion ◽  
Mitotic Cell ◽  
Intragenic Recombination ◽  
Cell Cycles ◽  
Normal Functions ◽  
Rad Genes ◽  
Radiation Repair

ABSTRACT In yeast, the functions controlled by radiation-repair genes RAD6, RAD50, RAD52 and RAD57 are essential for normal meiosis; diploids with lesions in these genes either fail to sporulate (rad6) or sporulate but produce inviable spores (rad50, 52, 57). Since RAD genes may control aspects of DNA metabolism, we attempted to define more precisely the role of each gene in meiosis, especially with regard to possible roles in premeiotic DNA replication and recombination. We constructed diploids singly homozygous for each of the four rad mutations, heteroallelic at his1 and heterozygous for a recessive canavanine-resistance marker. Each strain was exposed to sporulation-inducing conditions and monitored for (1) completion of mitotic cell cycles, (2) cell viability, (3)utilization of acetate for mass increases, (4)premeiotic DNA synthesis, (5) intragenic recombination at his1, and (6) formation of viable haploid spores. Control strains heterozygous for the rad mutations completed mitosis, metabolized acetate, replicated their DNA, and showed typically high levels of gene conversion and viable-spore formation. The mutant diploids also completed mitosis, utilized acetate, and carried out premeiotic DNA replication. The mutants, however, showed little or no meiotic gene conversion. The rad50, 52 and 57 strains sporulated, but the spores were inviable. The rad6 strain did not sporulate. The rad50, 52 and 57 strains exhibited viability losses that co-incided with the period of DNA synthesis, but not with later meiotic events; the rad6 strain did not lose viability. We propose that the normal functions specified by RAD50,52 and 57 are not essential for either the initial or terminal steps in meiosis, but are required for successful recombination. The rad6 strain may be recombination-defective, o r it may fail to progress past DNA replication in the overall sequence leading to formation and recovery of meiotic recombinants.

scholarly journals Prevention of DNA Rereplication Through a Meiotic Recombination Checkpoint Response

2016 ◽  
Vol 6 (12) ◽  
pp. 3869-3881
Author(s):  
Nicole A Najor ◽  
Layne Weatherford ◽  
George S Brush
Keyword(s):  
Cell Cycle ◽  
Dna Replication ◽  
Protein Kinase ◽  
Meiotic Recombination ◽  
Mitotic Cell ◽  
Mitotic Cell Cycle ◽  
Cyclin Dependent Kinase ◽  
Checkpoint Response ◽  
Recombination Checkpoint ◽  
Dna Rereplication

Abstract In the budding yeast Saccharomyces cerevisiae, unnatural stabilization of the cyclin-dependent kinase inhibitor Sic1 during meiosis can trigger extra rounds of DNA replication. When programmed DNA double-strand breaks (DSBs) are generated but not repaired due to absence of DMC1, a pathway involving the checkpoint gene RAD17 prevents this DNA rereplication. Further genetic analysis has now revealed that prevention of DNA rereplication also requires MEC1, which encodes a protein kinase that serves as a central checkpoint regulator in several pathways including the meiotic recombination checkpoint response. Downstream of MEC1, MEK1 is required through its function to inhibit repair between sister chromatids. By contrast, meiotic recombination checkpoint effectors that regulate gene expression and cyclin-dependent kinase activity are not necessary. Phosphorylation of histone H2A, which is catalyzed by Mec1 and the related Tel1 protein kinase in response to DSBs, and can help coordinate activation of the Rad53 checkpoint protein kinase in the mitotic cell cycle, is required for the full checkpoint response. Phosphorylation sites that are targeted by Rad53 in a mitotic S phase checkpoint response are also involved, based on the behavior of cells containing mutations in the DBF4 and SLD3 DNA replication genes. However, RAD53 does not appear to be required, nor does RAD9, which encodes a mediator of Rad53, consistent with their lack of function in the recombination checkpoint pathway that prevents meiotic progression. While this response is similar to a checkpoint mechanism that inhibits initiation of DNA replication in the mitotic cell cycle, the evidence points to a new variation on DNA replication control.

scholarly journals CDK promotes interactions of Sld3 and Drc1 with Cut5 for initiation of DNA replication in fission yeast

2011 ◽  
Vol 22 (14) ◽  
pp. 2620-2633 ◽  
Author(s):  
Masayoshi Fukuura ◽  
Koji Nagao ◽  
Chikashi Obuse ◽  
Tatsuro S. Takahashi ◽  
Takuro Nakagawa ◽  
...  
Keyword(s):  
Dna Replication ◽  
Fission Yeast ◽  
Ternary Complex ◽  
Budding Yeast ◽  
S Phase ◽  
Replication Proteins ◽  
Cyclin Dependent Kinase ◽  
Replication Origins ◽  
Initiation Of Dna Replication

Cyclin-dependent kinase (CDK) plays essential roles in the initiation of DNA replication in eukaryotes. Although interactions of CDK-phosphorylated Sld2/Drc1 and Sld3 with Dpb11 have been shown to be essential in budding yeast, it is not known whether the mechanism is conserved. In this study, we investigated how CDK promotes the assembly of replication proteins onto replication origins in fission yeast. Phosphorylation of Sld3 was found to be dependent on CDK in S phase. Alanine substitutions at CDK sites decreased the interaction with Cut5/Dpb11 at the N-terminal BRCT motifs and decreased the loading of Cut5 onto replication origins. This defect was suppressed by overexpression of drc1+. Phosphorylation of a conserved CDK site, Thr-111, in Drc1 was critical for interaction with Cut5 at the C-terminal BRCT motifs and was required for loading of Cut5. In a yeast three-hybrid assay, Sld3, Cut5, and Drc1 were found to form a ternary complex dependent on the CDK sites of Sld3 and Drc1, and Drc1–Cut5 binding enhanced the Sld3–Cut5 interaction. These results show that the mechanism of CDK-dependent loading of Cut5 is conserved in fission yeast in a manner similar to that elucidated in budding yeast.

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